2H76

Crystal Structure of Thioredoxin Mutant D10E in Hexagonal (p61) Space Group

• PDB DOI: https://doi.org/10.2210/pdb2H76/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-06-01 Released: 2007-05-15 
• Deposition Author(s): Gavira, J.A., Godoy-Ruiz, R., Ibarra-Molero, B., Sanchez-Ruiz, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.268 
• R-Value Work: 0.195 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Crystal Structure of Thioredoxin Mutant D10E in Hexagonal (p61) Space Group

Godoy-Ruiz, R., Gavira, J.A., Ibarra-Molero, B., Sanchez-Ruiz, J.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.64 kDa 
• Atom Count: 1,810 
• Modelled Residue Count: 215 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	A, B	108	Escherichia coli	Mutation(s): 1  Gene Names: trxA
UniProt
Find proteins for P0AA25 (Escherichia coli (strain K12)) Explore P0AA25  Go to UniProtKB:  P0AA25

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.268 
• R-Value Work: 0.195 
• R-Value Observed: 0.202 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.17	α = 90
b = 103.17	β = 90
c = 41.834	γ = 120

Software Package:

Software Name	Purpose
SAINT	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction
SADABS	data scaling
XPREP	data reduction
Coot	model building
MolProbity	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Gavira, J.A., Godoy-Ruiz, R., Ibarra-Molero, B., Sanchez-Ruiz, J.M.

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2012-05-02
  Changes: Structure summary
• Version 1.4: 2017-10-18
  Changes: Refinement description
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations, Experimental preparation
• Version 1.6: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.7: 2024-10-30
  Changes: Structure summary